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41 #include "visibility.h"
48 #include "gmx_random.h"
55 /* Abstract type for stochastic dynamics */
56 typedef struct gmx_update *gmx_update_t;
58 /* Initialize the stochastic dynamics struct */
59 gmx_update_t init_update(FILE *fplog,t_inputrec *ir);
61 /* Store the random state from sd in state */
63 void get_stochd_state(gmx_update_t sd,t_state *state);
65 /* Set the random in sd from state */
67 void set_stochd_state(gmx_update_t sd,t_state *state);
69 /* Store the box at step step
70 * as a reference state for simulations with box deformation.
73 void set_deform_reference_box(gmx_update_t upd,
74 gmx_large_int_t step,matrix box);
77 void update_tcouple(FILE *fplog,
81 gmx_ekindata_t *ekind,
82 gmx_wallcycle_t wcycle,
89 void update_pcouple(FILE *fplog,
95 gmx_wallcycle_t wcycle,
100 void update_coords(FILE *fplog,
101 gmx_large_int_t step,
102 t_inputrec *inputrec, /* input record and box stuff */
106 rvec *f, /* forces on home particles */
110 gmx_ekindata_t *ekind,
112 gmx_wallcycle_t wcycle,
116 t_commrec *cr, /* these shouldn't be here -- need to think about it */
121 /* Return TRUE if OK, FALSE in case of Shake Error */
124 extern gmx_bool update_randomize_velocities(t_inputrec *ir, gmx_large_int_t step, t_mdatoms *md, t_state *state, gmx_update_t upd, t_idef *idef, gmx_constr_t constr);
127 void update_constraints(FILE *fplog,
128 gmx_large_int_t step,
129 real *dvdlambda, /* FEP stuff */
130 t_inputrec *inputrec, /* input record and box stuff */
131 gmx_ekindata_t *ekind,
136 rvec force[], /* forces on home particles */
142 gmx_wallcycle_t wcycle,
150 /* Return TRUE if OK, FALSE in case of Shake Error */
153 void update_box(FILE *fplog,
154 gmx_large_int_t step,
155 t_inputrec *inputrec, /* input record and box stuff */
159 rvec force[], /* forces on home particles */
163 gmx_wallcycle_t wcycle,
166 gmx_bool bFirstHalf);
167 /* Return TRUE if OK, FALSE in case of Shake Error */
169 void calc_ke_part(t_state *state,t_grpopts *opts,t_mdatoms *md,
170 gmx_ekindata_t *ekind,t_nrnb *nrnb,gmx_bool bEkinAveVel, gmx_bool bSaveOld);
172 * Compute the partial kinetic energy for home particles;
173 * will be accumulated in the calling routine.
176 * Ekin = SUM(i) 0.5 m[i] v[i] (x) v[i]
178 * use v[i] = v[i] - u[i] when calculating temperature
180 * u must be accumulated already.
182 * Now also computes the contribution of the kinetic energy to the
189 init_ekinstate(ekinstate_t *ekinstate,const t_inputrec *ir);
193 update_ekinstate(ekinstate_t *ekinstate,gmx_ekindata_t *ekind);
196 restore_ekinstate_from_state(t_commrec *cr,
197 gmx_ekindata_t *ekind,ekinstate_t *ekinstate);
199 void berendsen_tcoupl(t_inputrec *ir,gmx_ekindata_t *ekind,real dt);
201 void andersen_tcoupl(t_inputrec *ir,t_mdatoms *md,t_state *state, gmx_rng_t rng, real rate, t_idef *idef, int nblocks, int *sblock,gmx_bool *randatom, int *randatom_list, gmx_bool *randomize, real *boltzfac);
203 void nosehoover_tcoupl(t_grpopts *opts,gmx_ekindata_t *ekind,real dt,
204 double xi[],double vxi[],t_extmass *MassQ);
207 t_state *init_bufstate(const t_state *template_state);
209 void destroy_bufstate(t_state *state);
212 void trotter_update(t_inputrec *ir, gmx_large_int_t step, gmx_ekindata_t *ekind,
213 gmx_enerdata_t *enerd, t_state *state, tensor vir, t_mdatoms *md,
214 t_extmass *MassQ, int **trotter_seqlist, int trotter_seqno);
217 int **init_npt_vars(t_inputrec *ir, t_state *state, t_extmass *Mass, gmx_bool bTrotter);
219 real NPT_energy(t_inputrec *ir, t_state *state, t_extmass *MassQ);
220 /* computes all the pressure/tempertature control energy terms to get a conserved energy */
222 void NBaroT_trotter(t_grpopts *opts, real dt,
223 double xi[],double vxi[],real *veta, t_extmass *MassQ);
225 void vrescale_tcoupl(t_inputrec *ir,gmx_ekindata_t *ekind,real dt,
226 double therm_integral[],
228 /* Compute temperature scaling. For V-rescale it is done in update. */
230 real vrescale_energy(t_grpopts *opts,double therm_integral[]);
231 /* Returns the V-rescale contribution to the conserved energy */
233 void rescale_velocities(gmx_ekindata_t *ekind,t_mdatoms *mdatoms,
234 int start,int end,rvec v[]);
235 /* Rescale the velocities with the scaling factor in ekind */
238 void update_annealing_target_temp(t_grpopts *opts,real t);
239 /* Set reference temp for simulated annealing at time t*/
241 real calc_temp(real ekin,real nrdf);
242 /* Calculate the temperature */
244 real calc_pres(int ePBC,int nwall,matrix box,tensor ekin,tensor vir,
246 /* Calculate the pressure tensor, returns the scalar pressure.
247 * The unit of pressure is bar.
250 void parrinellorahman_pcoupl(FILE *fplog,gmx_large_int_t step,
251 t_inputrec *ir,real dt,tensor pres,
252 tensor box,tensor box_rel,tensor boxv,
254 gmx_bool bFirstStep);
256 void berendsen_pcoupl(FILE *fplog,gmx_large_int_t step,
257 t_inputrec *ir,real dt,tensor pres,matrix box,
261 void berendsen_pscale(t_inputrec *ir,matrix mu,
262 matrix box,matrix box_rel,
263 int start,int nr_atoms,
264 rvec x[],unsigned short cFREEZE[],
267 void correct_ekin(FILE *log,int start,int end,rvec v[],
268 rvec vcm,real mass[],real tmass,tensor ekin);
269 /* Correct ekin for vcm */
276 #endif /* _update_h */